G4 CUT&Tag analysis mESC (ERCC WT and KO)

Simon Elsässer, Karolinska Institutet (2023)

Profile plots of promoters, enhancders and significant peaks determined by DESeq2.

bw_dir <- "/Volumes/DATA/DATA/Puck/bigwig/"

library("wigglescout")
library("ggpubr")
library("ggplot2")
library("DESeq2")

Loading required package: SummarizedExperiment
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Attaching package: ‘matrixStats’

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    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins,
    colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads,
    colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges,
    colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs,
    rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs,
    rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads,
    rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars

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Welcome to Bioconductor

    Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor,
    see 'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: ‘Biobase’

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library("dplyr")
library("ggrastr")

clean <- function (fn) {
  fn <- gsub(pattern = ".+/", "", x = fn)
  fn <- gsub(pattern = ".mm9.+", "", x = fn)
  fn <- gsub(pattern = ".mm39.+", "", x = fn)
  fn <- gsub(pattern = "_S.+", "", x = fn)
  fn <- gsub(pattern = "_combined.+", "", x = fn)
  fn <- gsub(pattern = "G4 CnT ", "", x = fn)
  fn <- gsub(pattern = "G4_CnT_", "", x = fn)
  fn <- gsub(pattern = "_batch2", "", x = fn)
  fn <- gsub(pattern = "-", " ", x = fn)
  fn <- gsub(pattern = "_", " ", x = fn)
  fn <- gsub(pattern = " HA ", " ", x = fn)
  fn <- gsub(pattern = "D1D6", "FANCJ-/-", x = fn)
  fn <- gsub(pattern = "P2D2", "DHX36-/-", x = fn)
  fn <- gsub(pattern = "P3D4", "FANCJ-/-DHX36-/-", x = fn)
  return(fn)
}

theme_blank <- theme(axis.line=element_blank(),
      axis.text.x=element_blank(),
      axis.text.y=element_blank(),
      axis.ticks=element_blank(),
      axis.title.x=element_blank(),
      axis.title.y=element_blank(),
      legend.position="none",
      panel.background=element_blank(),
      panel.border=element_blank(),
      panel.grid.major=element_blank(),
      panel.grid.minor=element_blank(),
      plot.background=element_blank())

G4.BWs <- list.files(bw_dir,pattern="G4_CnT_ERCC.+_R..bw",full.names = T)
R.BWs <- list.files(bw_dir,pattern="Rloop_CnT_ERCC.+_R..bw",full.names = T)

mypal <-c("cornflowerblue","orange","red2","#505050")
mypal2 <-c("darkorange2","darkorange2","#505050","#505050")

DJ peaks

non-DJ peaks

replicate consistency

ERCC KO vs WT

replicate consistency

ERCC KO vs WT

top DKO peaks

FANCJ diff peaks

R loops

Rloops DJ

Rloops nonDJ

Rloops FANCJ

facet(p2, facet.by = "name", ncol=6) + coord_cartesian(ylim=c(0,50)) + stat_compare_means(label.y = 45, aes(label = paste0("p=", after_stat(p.format)))) 

Warning: Removed 2 rows containing non-finite outside the scale range (`stat_ydensity()`).
Warning: Removed 2 rows containing non-finite outside the scale range (`stat_summary()`).
Warning: Removed 2 rows containing non-finite outside the scale range (`stat_compare_means()`).

ggsave('panels/panel_G4_Rloop_ERCCKO.pdf',p)

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